[gmx-users] position restrained minimization on the one part of a system

[Mark Abraham]

On 27/10/2011 12:28 AM, Atila Petrosian wrote:
> Dear Mark
>
> thanks for your reply
>
> you said "if pdb2gmx is able to treat the whole system in one pass, 
> then it will write such position restraint
> files automatically"
>
> in my system, what pdb2gmx includes are in below:
>
> ; Include forcefield parameters
> #include "amber03.ff/forcefield.itp"
>
> ; Include chain topologies
> #include "complex_Protein_chain_A.itp"
> #include "complex_DNA_chain_B.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_A.itp"
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre_Protein_chain_B.itp"

This is the kind of thing to which I was referring, but it appears you 
have edited your .top and removed the #endif lines that should match the 
#ifdef. Start again with pdb2gmx to generate a new .top, and then you 
will be able to choose your "define = -DPOSRES_xxx" to use position 
restraints on whichever part of the system you want with no need to ever 
touch a .top or .itp file.

Mark

>
> ; Include water topology
> #include "amber03.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "amber03.ff/ions.itp"
>
> [ system ]
> ; Name
> complex
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> DNA_chain_B         1
> SOL                        3500
>
>
> unfortunately, I don't know about step 1.
>
> please guide me about that.
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111027/598dbbaf/attachment.html>